help dg_sub_embed

dhbao at pegasus.rutgers.edu dhbao at pegasus.rutgers.edu
Wed Dec 31 17:24:40 EST 1997


Dear X-plorers: 

I am new in using x-plor. I try to calculate protein structure using NMR restrains with the protocol 
nmr/dg_sub_embed.inp. The structure file I used was generate by nmr/generate.inp ( read a 
sequence file instead of pdb file ) and the psf file then was used to generate a template using 
nmr/generate_template.inp. 

The problem is that the dg_sub_embed.inp always got a memory problem and then stop. Then I 
modified the protocol let the program only read three S-S bond restrains and no noe or dihedrals 
and the same problem happen again. Below is  tail of the output. Does anybody had the same 
problem? Please help me out. Thanks in advance. 

 
 X-PLOR> ! @g_protein_dihe.tbl                       {*Read dihedral angle restraints.*} 
 X-PLOR> 
 X-PLOR> 
 X-PLOR> 
 X-PLOR>{====>} 
 X-PLOR>               {*If protein contains S-S bridges, appropriately modify and *} 
 X-PLOR>               {*then uncomment the following lines.                       *} 
 X-PLOR>noe 
 NOE>   assign (resid  7 and name sg) (resid 131 and name sg)  2.02 0.1 0.1 
 SELRPN:      1 atoms have been selected out of   2163 
 SELRPN:      1 atoms have been selected out of   2163 
 NOE>   assign (resid  28 and name sg) (resid 69 and name sg)  2.02 0.1 0.1 
 SELRPN:      1 atoms have been selected out of   2163 
 SELRPN:      1 atoms have been selected out of   2163 
 NOE>   assign (resid 50 and name sg) (resid 103 and name sg)  2.02 0.1 0.1 
 SELRPN:      1 atoms have been selected out of   2163 
 SELRPN:      1 atoms have been selected out of   2163 
 NOE>end 
 X-PLOR> 
 X-PLOR> 
 X-PLOR>            {*Read template for pseudoatom correction and for target values*} 
 X-PLOR>            {*for conformational constraints (bonds, angles, etc.).        *} 
 X-PLOR>{===>} coor disp=refe @gen.pdb 
 COOR: coordinates read into REFE set 
 ASSFIL: file gen.pdb opened. 
 COOR>REMARK FILENAME="gen.pdb" 
 COOR>REMARK produced by nmr/generate_template.inp 
 COOR>REMARK DATE:31-Dec-97  12:44:00       created by user: bao 
 COOR>ATOM      1  CA  GLU     1      -6.514   0.776   0.784  1.00  0.00 
 COOR>ATOM      2  HA  GLU     1      -6.949  -0.174   0.519  1.00  0.00 
 X-PLOR> 
 X-PLOR> 
 X-PLOR>{===>} 
 X-PLOR>                                {*Store (sub)structure selection in store1.*} 
 X-PLOR>         {*The following substructure selection is typical for a protein;  *} 
 X-PLOR>         {*for nucleic acids try name p or name c3' or name c5' or name c1'*} 
 X-PLOR>         {*or name n9 or name n1 or name c2 or name c4 or name n3.         *} 
 X-PLOR> 
 X-PLOR>vector ident ( store1 ) (name ca or name ha or name n or name hn 
 SELRPN>                        or name c or name cb* or name cg*) 
 SELRPN:    905 atoms have been selected out of   2163 
 X-PLOR> 
 X-PLOR>                                     {*Energy flags: both NOEs and dihedral*} 
 X-PLOR>                                     {*angle restraints are included.      *} 
 X-PLOR> 
 X-PLOR>flags exclude * include bond angle dihedral improper vdw noe cdih end 
 X-PLOR> 
 X-PLOR>mmdg                                                {*Create bounds matrix.*} 
 MMDG>   reference=coordinates 
 MMDG>   storebounds                                       {*Store bounds matrix.*} 
 MMDG>end 
 DGSMOOT: number of connections: 23602 
 DGSMOOT: using sparse matrix bound smoothing algorithm. 
 DGSMOOT: max. size of network (upper, lower):   120   34 
 MMDG: storing smoothed bounds matrix in memory. 
        No metrization or embedding performed. 
 X-PLOR> 
 X-PLOR>                                      {*Include DG term for regularization.*} 
 X-PLOR>flags exclude * include dg end 
 X-PLOR>constraints interaction=( recall1 ) ( recall1 ) end 
 SELRPN:    905 atoms have been selected out of   2163 
 SELRPN:    905 atoms have been selected out of   2163 
 X-PLOR> 
 X-PLOR>evaluate ($count = 0) 
 EVALUATE: symbol $COUNT set to   0.000000E+00 (real) 
 X-PLOR> 
 X-PLOR>                {*The following loop produces a family of 10 substructures.*} 
 X-PLOR>{====>} 
 X-PLOR>while ($count < 10 ) loop main 
 NEXTCD: condition evaluated as true 
 X-PLOR> 
 X-PLOR>   evaluate ($count=$count+1) 
 EVALUATE: symbol $COUNT set to    1.00000     (real) 
 X-PLOR>   evaluate ($embedded = false) 
 EVALUATE: symbol $EMBEDDED set to FALSE (logical) 
 X-PLOR> 
 X-PLOR>                                      {*Loop until embedding is successful;*} 
 X-PLOR>                                      {*normally the success rate is high, *} 
 X-PLOR>                                      {*and it will work during the first  *} 
 X-PLOR>                                      {*pass.                              *} 
 X-PLOR>   while ($embedded = false) loop embed 
 NEXTCD: condition evaluated as true 
 X-PLOR>      mmdg 
 MMDG>         recallbounds                                  {*Get bounds matrix.*} 
 MMDG> 
 MMDG>         substructure=( recall1 ) 
 SELRPN:    905 atoms have been selected out of   2163 
 MMDG> 
 MMDG>         selection=( recall1 )                     {*Specify parameters    *} 
 SELRPN:    905 atoms have been selected out of   2163 
 MMDG>         scale=100.  exponent=2       {was scale=100. *for DG-regularization.*} 
 MMDG>      end 
 MMDG: no atoms will be metrized. 
 %ALLHP-err: too much memory requested. 
 Subroutine DIE called . Terminating 
-- 
 

******************************************************* 
 Donghui Bao             dhbao at pegasus.rutgers.edu 
 Dept. of Chemistry 
 Rutgers University 
 73 Warren St. 
 Newark, NJ 07102 
******************************************************* 
  



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